bioinformatics-data-skills

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Bioinformatics Data Skills

Author : Vince Buffalo
ISBN : 9781449367510
Genre : Computers
File Size : 47. 20 MB
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Learn the data skills necessary for turning large sequencing datasets into reproducible and robust biological findings. With this practical guide, you’ll learn how to use freely available open source tools to extract meaning from large complex biological data sets. At no other point in human history has our ability to understand life’s complexities been so dependent on our skills to work with and analyze data. This intermediate-level book teaches the general computational and data skills you need to analyze biological data. If you have experience with a scripting language like Python, you’re ready to get started. Go from handling small problems with messy scripts to tackling large problems with clever methods and tools Process bioinformatics data with powerful Unix pipelines and data tools Learn how to use exploratory data analysis techniques in the R language Use efficient methods to work with genomic range data and range operations Work with common genomics data file formats like FASTA, FASTQ, SAM, and BAM Manage your bioinformatics project with the Git version control system Tackle tedious data processing tasks with with Bash scripts and Makefiles

Bioinformatics Data Skills

Author : Vince Buffalo
ISBN : 1449367488
Genre : SCIENCE
File Size : 28. 95 MB
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Bioinformatics Data Skills Reproducible And Robust Research

Author : Felicity Howard
ISBN : 1684695023
Genre : Big data
File Size : 40. 94 MB
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Curriculum Applications In Microbiology Bioinformatics In The Classroom

Author : Mel Crystal Melendrez
ISBN : 9782889712687
Genre : Science
File Size : 26. 18 MB
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Bioinformatics Biocomputing And Perl

Author : Michael Moorhouse
ISBN : 9780470026458
Genre : Medical
File Size : 78. 82 MB
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Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today’s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material. Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease. Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples. Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet. Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.

Sequence Analysis And Modern C

Author : Hannes Hauswedell
ISBN : 9783030909901
Genre : Computers
File Size : 71. 6 MB
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This is a book about software engineering, bioinformatics, the C++ programming language and the SeqAn library. In the broadest sense, it will help the reader create better, faster and more reliable software by deepening their understanding of available tools, language features, techniques and design patterns. Every developer who previously worked with C++ will enjoy the in-depth chapter on important changes in the language from C++11 up to and including C++20. In contrast to many resources on Modern C++ that present new features only in small isolated examples, this book represents a more holistic approach: readers will understand the relevance of new features and how they interact in the context of a large software project and not just within a "toy example". Previous experience in creating software with C++ is highly recommended to fully appreciate these aspects. SeqAn3 is a new, re-designed software library. The conception and implementation process is detailed in this book, including a critical reflection on the previous versions of the library. This is particularly helpful to readers who are about to create a large software project themselves, or who are planning a major overhaul of an existing library or framework. While the focus of the book is clearly on software development and design, it also touches on various organisational and administrative aspects like licensing, dependency management and quality control.

Storing Digital Binary Data In Cellular Dna

Author : Rocky Termanini
ISBN : 9780128234587
Genre : Science
File Size : 22. 97 MB
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Storing Digital Binary Data into Cellular DNA demonstrates how current digital information storage systems have short longevity and limited capacity, also pointing out that their production and consumption of data exceeds supply. Author Rocky Termanini explains the DNA system and how it encodes vast amounts of data, then presents information on the emergence of DNA as a storage technology for the ever-growing stream of data being produced and consumed. The book will be of interest to a range of readers looking to understand this game-changing technology, including researchers in computer science, biomedical engineers, geneticists, physicians, clinicians, law enforcement and cybersecurity experts. Presents a comprehensive reference on the fascinating and emerging technology of DNA storage Helps readers understand key concepts on how DNA works as an information storage system Provides readers with key information on the technologies used to work with DNA data encoding, such as CRISPR Covers emerging areas of application and ethical concern, such as Smart Cities, cybercrime and cyberwarfare Includes coverage of synthesizing DNA-encoded data, sequencing DNA-encoded data, and fusing DNA with Digital Immunity Ecosystems (DIE)

Variant Calling

Author : Charlotte Ng
ISBN : 9781071622933
Genre : Science
File Size : 73. 19 MB
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This volume provides practical guidance on a variety of techniques and steps to ensure successful variant calling. Chapters detail methods for variant calling from single-nucleotide variants to structural variants, variant calling in specialized data types such as RNA-seq and UMI-tagged sequencing, alignment-free genotyping and SNP calling, variant detection in single-cell DNA sequencing data, variant annotation, and preanalytical quality control to ensure successful variant calling. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists step-by-step protocol to execute the algorithms, describes the input and output data, and includes tips on troubleshooting and known pitfalls. Authoritative and cutting-edge, Variant Calling: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.

Genome Data Analysis

Author : Ju Han Kim
ISBN : 9789811319426
Genre : Science
File Size : 51. 80 MB
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This textbook describes recent advances in genomics and bioinformatics and provides numerous examples of genome data analysis that illustrate its relevance to real world problems and will improve the reader’s bioinformatics skills. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine learning algorithms using R and Python are demonstrated for gene-expression microarrays, genotyping microarrays, next-generation sequencing data, epigenomic data, and biological network and semantic analyses. In addition, detailed attention is devoted to integrative genomic data analysis, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and integrated management of biomolecular databases. The textbook is primarily intended for life scientists, medical scientists, statisticians, data processing researchers, engineers, and other beginners in bioinformatics who are experiencing difficulty in approaching the field. However, it will also serve as a simple guideline for experts unfamiliar with the new, developing subfield of genomic analysis within bioinformatics.

Essential Computing Skills For Biologists

Author : Wang Ziling
ISBN : 9781848169265
Genre : Computers
File Size : 71. 47 MB
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This is a handbook of methods and protocols for biologists. It aimed at undergraduate, graduate students and researchers originally trained in biological or medical sciences who need to know how to access the data archives of genomes, proteins, metabolites, gene expression profiles and the questions these data and tools can answer. For each chapter, the conceptual and experimental background is provided, together with specific guidelines for handling raw data, including preprocessing and analysis. The content is structured into three parts. Part one introduces basic knowledge about popular bioinformatics tools, databases and web resources. Part two presents examples of omics bioinformatics applications. Part three provides basic statistical analysis skills and programming skills needed to handle and analyze omics datasets.

Developing Bioinformatics Computer Skills

Author : Cynthia Gibas
ISBN : 1565926641
Genre : Computers
File Size : 64. 43 MB
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Offers a structured approach to biological data and the computer tools needed to analyze it, covering UNIX, databases, computation, Perl, data mining, data visualization, and tailoring software to suit specific research needs.

R Bioinformatics Cookbook

Author : Dan MacLean
ISBN : 1789950694
Genre : Computers
File Size : 89. 61 MB
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Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to handle biological data using real-world examples Represent biological data with advanced visualizations suitable for research and publications Handle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analyses Book Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you'll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you'll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learn Employ Bioconductor to determine differential expressions in RNAseq data Run SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and Indels Use ggplot to create and annotate a range of visualizations Query external databases with Ensembl to find functional genomics information Execute large-scale multiple sequence alignment with DECIPHER to perform comparative genomics Use d3.js and Plotly to create dynamic and interactive web graphics Use k-nearest neighbors, support vector machines and random forests to find groups and classify data Who this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.

Bioinformatics

Author : David W. Mount
ISBN : 0879697121
Genre : Science
File Size : 82. 11 MB
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As more species' genomes are sequenced, computational analysis of these data has become increasingly important. The second, entirely updated edition of this widely praised textbook provides a comprehensive and critical examination of the computational methods needed for analyzing DNA, RNA, and protein data, as well as genomes. The book has been rewritten to make it more accessible to a wider audience, including advanced undergraduate and graduate students. New features include chapter guides and explanatory information panels and glossary terms. New chapters in this second edition cover statistical analysis of sequence alignments, computer programming for bioinformatics, and data management and mining. Practically oriented problems at the ends of chapters enhance the value of the book as a teaching resource. The book also serves as an essential reference for professionals in molecular biology, pharmaceutical, and genome laboratories.

Introduction To Bioinformatics With R

Author : Edward Curry
ISBN : 9781351015301
Genre : Science
File Size : 76. 15 MB
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In biological research, the amount of data available to researchers has increased so much over recent years, it is becoming increasingly difficult to understand the current state of the art without some experience and understanding of data analytics and bioinformatics. An Introduction to Bioinformatics with R: A Practical Guide for Biologists leads the reader through the basics of computational analysis of data encountered in modern biological research. With no previous experience with statistics or programming required, readers will develop the ability to plan suitable analyses of biological datasets, and to use the R programming environment to perform these analyses. This is achieved through a series of case studies using R to answer research questions using molecular biology datasets. Broadly applicable statistical methods are explained, including linear and rank-based correlation, distance metrics and hierarchical clustering, hypothesis testing using linear regression, proportional hazards regression for survival data, and principal component analysis. These methods are then applied as appropriate throughout the case studies, illustrating how they can be used to answer research questions. Key Features: · Provides a practical course in computational data analysis suitable for students or researchers with no previous exposure to computer programming. · Describes in detail the theoretical basis for statistical analysis techniques used throughout the textbook, from basic principles · Presents walk-throughs of data analysis tasks using R and example datasets. All R commands are presented and explained in order to enable the reader to carry out these tasks themselves. · Uses outputs from a large range of molecular biology platforms including DNA methylation and genotyping microarrays; RNA-seq, genome sequencing, ChIP-seq and bisulphite sequencing; and high-throughput phenotypic screens. · Gives worked-out examples geared towards problems encountered in cancer research, which can also be applied across many areas of molecular biology and medical research. This book has been developed over years of training biological scientists and clinicians to analyse the large datasets available in their cancer research projects. It is appropriate for use as a textbook or as a practical book for biological scientists looking to gain bioinformatics skills.

Practical Skills In Biomolecular Sciences

Author : Robert H. Reed
ISBN : UOM:39015060039362
Genre : Business & Economics
File Size : 56. 19 MB
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"Practical Skills in Biomolecular Sciences""" Laboratory and field studies are essential components of undergraduate training in the life sciences. Practical work must be fully understood and effectively presented, but many students under-perform because they lack basic laboratory skills. This book, now in its second edition, continues to provide students with easy-to-use guidance for laboratory and field studies, but in addition it now covers broader transferable skills. As a result the new edition provides guidance and support over the entire range of a typical undergraduate courses in biomolecular sciences. "New features for the second edition " A new section at the front of the book on Study and Examination skills, including new chapters on time management, working with others, note taking, revising, assessment and exams, and preparing a "cv." New chapters on bioinformatics and on the preparation and use of calibration curves. Updated material on the use of the Internet and World Wide Web. New material on evaluating information A a vital skill for todayAs students. New material in the numeracy and statistics chapters to provide greater support and guidance. Every chapter has study exercises to reinforce learning with problems and practical exercises. Answers are given at the back of the book for all exercises. Every chapter is supported by a section giving printed and electronic sources for further study. " Retained features from previous edition " Worked examples and "how to" boxes that set out the essential procedures in a step-by-step manner. Key points highlighting critical features of methodology. Use of margin tips, definitions and illustrations. Use of two-colour text throughout the book. Practical Skills in Biomolecular Sciences is an indispensable book for undergraduate students in a range of subjects including biochemistry, genetics, molecular biology and biomedical sciences. It is also a valuable resource for teachers of these subjects in colleges and secondary schools.

Reproducible Bioinformatics With Python

Author : Ken Youens-Clark
ISBN : 1098100883
Genre : Computers
File Size : 87. 61 MB
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Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and postdoc researchers who've never learned basic programming skills. This practical guide shows how to exploit the best parts of Python for solving problems in biology while also creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates how to write effective Python code and how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools--such as linters, formatters, type checkers, and tests--to write documented and tested programs. Create command-line Python programs that document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures (strings, lists, and sets) and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA, FASTQ, and SwissProt Find patterns of text using regular expressions Use higher-order functions in Python like filter() and map()

Mastering Perl For Bioinformatics

Author : James Tisdall
ISBN : 9781449390907
Genre : Computers
File Size : 24. 12 MB
Format : PDF
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Historically, programming hasn't been considered a critical skill for biologists. But now, with access to vast amounts of biological data contained in public databases, programming skills are increasingly in strong demand in biology research and development. Perl, with its highly developed capacities in string handling, text processing, networking, and rapid prototyping, has emerged as the programming language of choice for biological data analysis.Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics.The range of topics covered in Mastering Perl for Bioinformatics prepares the reader for enduring and emerging developments in critical areas of bioinformatics programming such as: Gene finding String alignment Methods of data storage and retrieval (SML and databases) Modeling of networks (graphs and Petri nets) Graphics (Tk) Parallelization Interfacing with other programming languages Statistics (PDL) Protein structure determination Biological models of computation (DNA Computers) Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.

Developing Bioinformatics Computer Skills

Author : Cynthia Gibas
ISBN : 0613912640
Genre : Computers
File Size : 36. 29 MB
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Offers a structured approach to biological data and the computer tools needed to analyze it, covering UNIX, databases, computation, Perl, data mining, data visualization, and tailoring software to suit specific research needs.

A Bioinformatics Discovery Oriented Computing Framework

Author : Jake Yue Chen
ISBN : MINN:31951P007547096
Genre :
File Size : 86. 4 MB
Format : PDF
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Science

Author : John Michels (Journalist)
ISBN : MINN:31951P009971378
Genre : Science
File Size : 89. 21 MB
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